DESeq2 load failed for Bioconductor ver 3.9
1
0
Entering edit mode
@biancaineshoch-20772
Last seen 4.9 years ago

Hello all.

I'm currently having issues loading DESeq2 into R version 3.6. I upgraded Bioconductor from version 3.7 to the latest version, 3.9. I am using my school's server to conduct RNA-Seq analysis.

Here is the error message that I receive:

> library(DESeq2)
Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘Hmisc’
In addition: Warning message:
replacing previous import ‘Biobase::dims’ by ‘BiocGenerics::dims’ when loading ‘DESeq2’

Here is the sessionInfo():

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] org.Hs.eg.db_3.8.2
 [2] PoiClaClu_1.0.2.1
 [3] RColorBrewer_1.1-2
 [4] pheatmap_1.0.12
 [5] GenomicAlignments_1.16.0
 [6] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.6
 [7] GenomicFeatures_1.36.0
 [8] AnnotationDbi_1.46.0
 [9] stringr_1.4.0
[10] stringi_1.4.3
[11] Rsamtools_1.32.3
[12] Biostrings_2.48.0
[13] XVector_0.20.0
[14] SummarizedExperiment_1.10.1
[15] DelayedArray_0.6.6
[16] BiocParallel_1.14.2
[17] matrixStats_0.54.0
[18] Biobase_2.40.0
[19] GenomicRanges_1.32.7
[20] GenomeInfoDb_1.20.0
[21] IRanges_2.14.12
[22] S4Vectors_0.18.3
[23] BiocGenerics_0.30.0

loaded via a namespace (and not attached):
 [1] progress_1.2.1         lattice_0.20-38        colorspace_1.4-1
 [4] rtracklayer_1.40.6     blob_1.1.1             XML_3.98-1.19
 [7] rlang_0.3.4            DBI_1.0.0              bit64_0.9-7
[10] GenomeInfoDbData_1.2.1 zlibbioc_1.26.0        munsell_0.5.0
[13] gtable_0.3.0           memoise_1.1.0          biomaRt_2.40.0
[16] Rcpp_1.0.1             xtable_1.8-4           scales_1.0.0
[19] BiocManager_1.30.4     annotate_1.62.0        bit_1.1-14
[22] hms_0.4.2              digest_0.6.18          grid_3.6.0
[25] tools_3.6.0            bitops_1.0-6           magrittr_1.5
[28] RCurl_1.95-4.12        RSQLite_2.1.1          crayon_1.3.4
[31] pkgconfig_2.0.2        Matrix_1.2-17          prettyunits_1.0.2
[34] assertthat_0.2.1       httr_1.4.0             R6_2.4.0
[37] compiler_3.6.0
deseq2 • 2.5k views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 17 hours ago
United States

DESeq2 depends on Hmisc, so that is the main problem here.

What happens when you try to install DESeq2:

BiocManager::install("DESeq2")

If you do not have permissions, you may have to ask an administrator to reinstall for you.

ADD COMMENT
0
Entering edit mode

Thank you for your quick reply! My PI has root access and got a similar error, so I'm not sure my problem is permissions. The entire output stream is too long for me to include, so I cut to the first fatal error. Here is the result of installing DESeq2:

> > BiocManager::install("DESeq2") Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26) Installing package(s) 'DESeq2' also installing the dependencies ‘vctrs’, ‘pillar’, ‘tibble’, ‘viridis’,
> ‘ggplot2’, ‘Hmisc’ trying URL
> 'https://cloud.r-project.org/src/contrib/vctrs_0.1.0.tar.gz' Content
> type 'application/x-gzip' length 412633 bytes (402 KB)
> ================================================== downloaded 402 KB trying URL
> 'https://cloud.r-project.org/src/contrib/Hmisc_4.2-0.tar.gz' Content
> type 'application/x-gzip' length 732731 bytes (715 KB)
> ================================================== downloaded 715 KB trying URL
> 'https://bioconductor.org/packages/3.9/bioc/src/contrib/DESeq2_1.24.0.tar.gz'
> Content type 'application/x-gzip' length 2056901 bytes (2.0 MB)
> ================================================== downloaded 2.0 MB
> * installing *source* package ‘vctrs’ ...
> ** package ‘vctrs’ successfully unpacked and MD5 sums checked
> ** using staged installation
> ** libs gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c compare.c -o compare.o In file included from vctrs.h:2:0,
>                  from compare.c:1: /usr/share/R/include/R.h:55:80: fatal error: stdlib.h: No such file or directory compilation
> terminated. /usr/lib/R/etc/Makeconf:167: recipe for target 'compare.o'
> failed make: *** [compare.o] Error 1 ERROR: compilation failed for
> package ‘vctrs’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/vctrs’ ERROR: dependency ‘vctrs’ is not available for package ‘pillar’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/pillar’ ERROR: dependency ‘pillar’ is not available for package ‘tibble’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/tibble’ ERROR: dependency ‘tibble’ is not available for package ‘ggplot2’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/ggplot2’ ERROR: dependency ‘ggplot2’ is not available for package ‘viridis’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/viridis’ ERROR: dependencies ‘ggplot2’, ‘viridis’ are not available for package
> ‘Hmisc’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/Hmisc’ ERROR: dependencies ‘ggplot2’, ‘Hmisc’ are not available for package ‘DESeq2’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/DESeq2’ The downloaded source packages are in
>         ‘/tmp/RtmpfDJ5u3/downloaded_packages’ installation path not writeable, unable to update packages: acepack, ade4,   affy, affyio,
> askpass, backports, base64enc, bdsmatrix, bibtex, bindrcpp,   Biobase,
> BiocParallel, Biostrings, bit, bit64, bitops, car, caTools,  
> checkmate, colorspace, covr, curl, data.table, DelayedArray, deldir,
> diffobj,   digest, ellipsis, fansi, fastmatch, FNN, freetypeharfbuzz,
> fs, gdtools, gee,   GenomicAlignments, GenomicRanges, git2r, glue,
> kernlab, ks, later, lazyeval, leaps,   openxlsx, pcaMethods, pkgload,
> plyr, png, polysat, preprocessCore, pROC,   reshape2, reticulate, rgl,
> rlang, Rmpi, RSQLite, rtracklayer, Rwave,   SummarizedExperiment,
> edgeR, effects, expm, irlba, lme4, lmtest, locfit, maptools,  
> foreign, genefilter, GOstats, graph, gss, KernSmooth, lattice, MASS,
> Matrix,   RcppParallel, Rgraphviz, rmutil, spatial, stable, statip,
> survival, sva 

> Warning messages: 1: In install.packages(pkgs = doing,
> lib = lib, repos = repos, ...) :   installation of package ‘vctrs’ had
> non-zero exit status 2: In install.packages(pkgs = doing, lib = lib,
> repos = repos, ...) :   installation of package ‘pillar’ had non-zero
> exit status 3: In install.packages(pkgs = doing, lib = lib, repos =
> repos, ...) :   installation of package ‘tibble’ had non-zero exit
> status 4: In install.packages(pkgs = doing, lib = lib, repos = repos,
> ...) :   installation of package ‘ggplot2’ had non-zero exit status 5:
> In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :  
> installation of package ‘viridis’ had non-zero exit status 6: In
> install.packages(pkgs = doing, lib = lib, repos = repos, ...) :  
> installation of package ‘Hmisc’ had non-zero exit status 7: In
> install.packages(pkgs = doing, lib = lib, repos = repos, ...) :  
> installation of package ‘DESeq2’ had non-zero exit status
ADD REPLY
0
Entering edit mode

Looks like the problem starts with vctrs:

fatal error: stdlib.h: No such file or directory compilation terminated. /usr/lib/R/etc/Makeconf:167: recipe for target 'compare.o' failed make: * [compare.o] Error 1 ERROR: compilation failed for package ‘vctrs’

Not sure how you could fix on your system...

DESeq2 install fine on Ubuntu for many users I know (myself included).

ADD REPLY
0
Entering edit mode

Hmm. I'll continue to troubleshoot then. Thanks for your help, I'm a big fan of your work.

ADD REPLY
0
Entering edit mode

Hmm. I'll continue to troubleshoot then. Thanks for your help, I'm a big fan of your work.

ADD REPLY
0
Entering edit mode

My guess is that you have updated your OS or compilers after installing R, and the best bet would be to re-install R. Also simplify the problem to tackling the first failure -- BiocManager::install("vctrs")

ADD REPLY

Login before adding your answer.

Traffic: 656 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6